You make a good point. The IRS will receive Forms 1099-R that indicate how much was actually distributed from all of your accounts and they will be able to see that the amount shown on line 53 is more than the total of the Forms 1099-R you received and reported on Form 1040. However, I'm not sure that the IRS scrutinizes line 53 to that extent. If it makes you more comfortable, you could amend the Form 5329 to reduce the original amounts on lines 52 and 53 each by RMD2 and file it along with Form 1040X where you can provide explanation and show that this results in no changes to any of the amounts elsewhere on your tax return. The alternative is to just do nothing and provide explanation if the IRS ever questions this. Since you filed Form 5329 Part IV, the IRS has only until April 15, 2023 years to question whether or not you had any excess accumulation for 2019.
Just don't amend until your originally filed tax return has been processed by the IRS.
